Tools

• data
• software
• computer

Tools

• data
• software
• computer

Data

Can change over time (months or years)

Data

Custom dataset

You can even build your own reference genome(s)

• unkown species
• unkown genes
• …

Incoming data

Your lab can generate data over time

and

you must re-analyze it multiple times or combining it in many ways

Tools

• data
• software
• computer

Software

They transform data

Software

Each transformation has an input and an output

Software

The output of the previous transformation is the input for the next one

Software

There are many tools for many purposes and our duty is to combine them in a proper way

Software

• Operating System (OS)
• Applications
• Bioinformatics Applications

Software: OS

Linux

OS

OS

• Linux is open source

Its core code can be inspected and you can contribute !

torvalds/linux

OS

• Linux is open source

It is a very very stable system

Our cluster uptime is about Years

OS

W3Tech

OS

• Standalone or Remote

You can install Linux main OS or access a remote machine by network

OS

OS

OS

• Multi user
  • Disk
  • Memory
  • CPU

Most of the time you share resources with others

OS

• Multi user
  • Disk ( HDD: long term storage )
  • Memory ( RAM: volatile )
  • CPU ( engine )

Most of the time you share resources with others

OS

• Cluster of thousands of machines

OS

• Open Source
• Standalone or Remote
• Multi User
• Cluster of thousands of machines
• Stable
• Huge communities

Software: Applications

Whatever action you are doing through a computer you are going to use a software somewhere

Applications

In any case we have 2 best friends:

• An Interface
• An Editor

Interfaces

• Graphical User Interface
• The ugly terminal

Interfaces

• Graphical User Interface (ICONS !!!! Mouse !!!!)
• The ugly terminal

Interfaces

• Graphical User Interface
• The ugly terminal

Interfaces

The winner is ?

Interfaces

Terminal

You can instruct the machine to do whatever you want using the keyboard typing commands.

Editor

Editor

Terminal

With the terminal you can even write documents, text files.

NOT WORD FILES!!!

The Bash

It is a shell which interprets your commands and acts appropriately

• you will love it

The Bash

It is a shell which interprets your command and act appropriately

• you will hate it

The Bash

ls -la

The Bash

ls -l /root

The Bash

Write a file called “myfile.txt” with gedit and read it with the terminal

cat myfile.txt

The Bash

Copy a file

cp myfile.txt myfile.backup.txt

now do a ls

The Bash

Move a file aka Rename

mv myfile.txt MyFile.txt

now do a ls

The Bash

Connect to your own machine

ssh user@localhost

if you get a message like this:

The authenticity of host 'localhost (::1)' can't be established.
ECDSA key fingerprint is SHA256:Zf595J6gKYjVYVD3R/E1AnQmsLu7QB+Ff1kmBn7vdKo.
Are you sure you want to continue connecting (yes/no)?

Type yes

The Bash

Connect to a server

ssh user@192.168.200.213

now list all the connected users

who

There are many users all w/the same name

The Bash

Using applications

STAR --help

Installing programs

The functionalities of a computer can be extended installing software

Installing programs

1. Ubuntu/Debian packages list or apt search
2. Conda packages. search or conda search
3. Linuxbrew. List or brew search
4. From specialized archives: e.g. pip
5. Compile the program

Ubuntu packages

• Lots of packages ready apt-get install ne
• Very robust
• Additional packages with PPAs add-apt-repository ppa:user/ppa-name
  • Not very useful for science

Advantages

• Safe and efficient
• Easy to rebuild from source

Cons

• Sometimes outdated (Ubuntu LTS are released every 2 years)

Conda packages

• Must be downloaded and installed (with bash)
• Relies on channels
  • base with installation
  • bioconda: bioinformatics programs
  • conda-forge: misc programs
• Not very robust/stable

Advantages

• Programs are usually the latest version

Cons

• Needs update to config files (~/.bashrc)
• Weird interactions with system programs/libraries
• Messes up with $PATH (e.g. shebang)

Linuxbrew packages

• Must be downloaded and installed
• Only one source of packages
• Similar to conda
  • fewer packages

Conda

On our system is already installed by the procedure is quite easy if you start from scratch.

Conda

You can start creating a conda environemnt.

Conda

A conda environment let’s you install and use software softly separated by the original system

conda create -n unimiPhD

Bioinformatic Applications

Then you are ready to install the application for RNA-seq

Bioinformatic Applications

conda install -y -c bioconda \
                 fastqc=0.11.8 \
                 trimmomatic=0.38 \
                 samtools=1.9 \
                 star=2.6.1b

Tools

• data
• software
• computer

Computer

• Local
• Remote
• Physical
• Virtual
• Cloud